refactor(docs): move from reST to Markdown (#703)

.github/workflows/ci.yml

@@ -168,48 +168,8 @@ jobs:
     runs-on: ubuntu-20.04
     strategy:
       matrix:
-        include:
-          - testenv: lowest
-            python: '3.6'
-
-          - testenv: release
-            python: '3.6'
-
-          - testenv: lowest
-            python: '3.7'
-
-          - testenv: release
-            python: '3.7'
-
-          - testenv: lowest
-            python: '3.8'
-
-          - testenv: release
-            python: '3.8'
-
-          - testenv: lowest
-            python: '3.9'
-
-          - testenv: release
-            python: '3.9'
-
-          - testenv: lowest
-            python: '3.10'
-
-          - testenv: release
-            python: '3.10'
-
-          - testenv: lowest
-            python: '3.11'
-
-          - testenv: release
-            python: '3.11'
-
-          - testenv: lowest
-            python: '3.12'
-
-          - testenv: release
-            python: '3.12'
+        testenv: [lowest, release]
+        python: ['3.6', '3.7', '3.8', '3.9', '3.10', '3.11', '3.12']
     steps:
       - uses: actions/checkout@v3
 
@@ -224,10 +184,10 @@ jobs:
           pip install wheel
           pip install requirements-builder
           if [[ ${{ matrix.testenv }} == lowest ]]; then
-          requirements-builder -e all --level=min --req requirements-dev.txt setup.py > .lowest-requirements.txt
+          requirements-builder -e tests --level=min --req requirements-dev.txt setup.py > .lowest-requirements.txt
           fi
           if [[ ${{ matrix.testenv }} == release ]]; then
-          requirements-builder -e all --level=pypi --req requirements-dev.txt setup.py > .release-requirements.txt
+          requirements-builder -e tests --level=pypi --req requirements-dev.txt setup.py > .release-requirements.txt
           fi
 
       - name: Install Python dependencies

AUTHORS.md

@@ -0,0 +1,22 @@
+# Authors
+
+The list of contributors in alphabetical order:
+
+- [Adelina Lintuluoto](https://orcid.org/0000-0002-0726-1452)
+- [Audrius Mecionis](https://orcid.org/0000-0002-3759-1663)
+- [Anton Khodak](https://orcid.org/0000-0003-3263-4553)
+- [Camila Diaz](https://orcid.org/0000-0001-5543-797X)
+- [Daniel Prelipcean](https://orcid.org/0000-0002-4855-194X)
+- [Diego Rodriguez](https://orcid.org/0000-0003-0649-2002)
+- [Dinos Kousidis](https://orcid.org/0000-0002-4914-4289)
+- [Giuseppe Steduto](https://orcid.org/0009-0002-1258-8553)
+- [Harri Hirvonsalo](https://orcid.org/0000-0002-5503-510X)
+- [Jan Okraska](https://orcid.org/0000-0002-1416-3244)
+- [Leticia Wanderley](https://orcid.org/0000-0003-4649-6630)
+- [Marco Donadoni](https://orcid.org/0000-0003-2922-5505)
+- [Marco Vidal](https://orcid.org/0000-0002-9363-4971)
+- [Matthew Feickert](https://orcid.org/0000-0003-4124-7862)
+- [Rokas Maciulaitis](https://orcid.org/0000-0003-1064-6967)
+- [Sinclert Perez](https://www.linkedin.com/in/sinclert)
+- [Tibor Simko](https://orcid.org/0000-0001-7202-5803)
+- [Vladyslav Moisieienkov](https://orcid.org/0000-0001-9717-0775)

CHANGELOG.md

@@ -0,0 +1,220 @@
+# Changelog
+
+## 0.9.2 (2023-12-19)
+
+- Changes `validate` command to show detailed errors when the specification file is not a valid YAML file.
+- Changes the validation of specification files to show improved validation warnings, which also indicate where unexpected properties are located in the file.
+- Fixes `create_workflow_from_json` API function to always load and send the workflow specification to the server.
+- Fixes `list` command to accept case-insensitive column names when sorting the returned workflow runs via the `--sort` option.
+- Fixes `run` wrapper command for workflows that do not contain `inputs` clause in their specification.
+
+## 0.9.1 (2023-09-27)
+
+- Adds support for Python 3.12.
+- Adds `prune` command to delete all intermediate files of a given workflow. Use with care.
+- Changes `open` command to inform user about the auto-closure of interactive sessions after a certain inactivity timeout.
+- Changes `validate` command to display non-critical validation warnings when checking the REANA specification file.
+- Fixes `list` command to correctly list workflows when sorting them by their run number or by the size of their workspace.
+- Fixes `du` command help message typo.
+- Fixes `validation --environments` command to correctly handle fully-qualified image names.
+
+## 0.9.0 (2023-01-26)
+
+- Adds support for Python 3.11.
+- Adds support for `.gitignore` and `.reanaignore` to specify files that should not be uploaded to REANA.
+- Adds `retention-rules-list` command to list the retention rules of a workflow.
+- Changes REANA specification loading and validation functionalities by porting some of the logic to `reana-commons`.
+- Changes `create` and `restart` commands to always upload the REANA specification file.
+- Changes `delete` command to always delete the workflow's workspace.
+- Changes `delete_workflow` Python API function to always delete the workflow's workspace.
+- Changes `download` command to add the possibility to write files to the standard output via `-o -` option.
+- Changes `list` command to hide deleted workflows by default.
+- Changes `list` command to allow displaying deleted workflows via `--all` and `--show-deleted-runs` options.
+- Changes `list` and `status` commands to allow displaying the duration of workflows with the `--include-duration` option.
+- Changes `mv` command to allow moving files while a workflow is running.
+- Changes `upload` command to prevent uploading symlinks.
+- Changes `validation --environment` command to use Docker registry v2 APIs to check that a Docker image exists in DockerHub.
+- Fixes `list` command to highlight the workflow specified in `REANA_WORKON` correctly.
+- Fixes `secrets-delete` command error message when deleting non existing secrets.
+- Fixes `start` command to report failed workflows as errors.
+- Fixes `start` and `run` commands to correctly follow the execution of the workflow until termination.
+- Fixes `status` command to respect output format provided by the `--format` option.
+- Fixes `upload` command to report when input directories are listed under the `files` section in the REANA specification file and vice versa.
+- Fixes `validate --environment` command to detect illegal whitespace characters in Docker image names.
+
+## 0.8.1 (2022-02-15)
+
+- Adds support for creating reana-client standalone AppImage executables.
+- Adds support for Python 3.10.
+- Adds workflow name validation for `create_workflow_from_json()` Python API function.
+- Fixes formatting of error messages and sets appropriate exit status codes.
+
+## 0.8.0 (2021-11-24)
+
+- Adds support for running and validating Snakemake workflows.
+- Adds support for `outputs.directories` in `reana.yaml` allowing to easily download output directories.
+- Adds new command `quota-show` to retrieve information about total CPU and Disk usage and quota limits.
+- Adds new command `info` that retrieves general information about the cluster, such as available workspace path settings.
+- Changes `validate` command to add the possibility to check the workflow against server capabilities such as desired workspace path via `--server-capabilities` option.
+- Changes `list` command to add the possibility to filter by workflow status and search by workflow name via `--filter` option.
+- Changes `list` command to add the possibility to filter and display all the runs of a given workflow via `-w` option.
+- Changes `list` command to stop including workflow progress and workspace size by default. Please use new options `--include-progress` and `--include-workspace-size` to show this information.
+- Changes `list --sessions` command to display the status of interactive sessions.
+- Changes `logs` command to display also the start and finish times of individual jobs.
+- Changes `ls` command to add the possibility to filter by file name, size and last-modified values via `--filter` option.
+- Changes `du` command to add the possibility filter by file name and size via `--filter` option.
+- Changes `delete` command to prevent hard-deletion of workflows.
+- Changes Yadage workflow specification loading to be done in `reana-commons`.
+- Changes CWL workflow engine to `cwltool` version `3.1.20210628163208`.
+- Removes support for Python 2.7. Please use Python 3.6 or higher from now on.
+
+## 0.7.5 (2021-07-05)
+
+- Changes workflow validation to display more granular output.
+- Changes workflow parameters validation to warn about misused parameters for each step.
+- Changes dependencies to unpin six so that client may be installed in more contexts.
+- Fixes environment image validation not to test repetitively the same image.
+- Fixes `upload_to_server()` Python API function to silently skip uploading in case of none-like inputs.
+
+## 0.7.4 (2021-04-28)
+
+- Adds support of wildcard patterns to `ls` command.
+- Adds support of directory download and wildcard patterns to `download` command.
+- Changes `list` command to include deleted workflows by default.
+- Fixes environment image validation info message where UIDs were switched.
+
+## 0.7.3 (2021-03-24)
+
+- Adds validation of workflow input parameters to the `validate` command.
+- Adds optional validation of workflow environment images (`--environments`) to the `validate` command.
+
+## 0.7.2 (2021-01-15)
+
+- Adds support for Python 3.9.
+- Fixes exception handling when uploading files.
+- Fixes minor code warnings.
+- Fixes traling slash issue from user exported REANA_SERVER_URL.
+
+## 0.7.1 (2020-11-10)
+
+- Changes `ping` command output to include REANA client and server version information.
+- Fixes `upload` command to properly display errors.
+
+## 0.7.0 (2020-10-20)
+
+- Adds option to `logs` command to filter job logs according to compute backend, docker image, status and step name.
+- Adds new `restart` command to restart previously run or failed workflows.
+- Adds possibility to specify operational options in the `reana.yaml` of the workflow.
+- Fixes user experience by preventing dots as part of the workflow name to avoid confusion with restart runs.
+- Changes `du` command output format.
+- Changes file loading to optimise CLI performance.
+- Changes `logs` command to enhance formatting using marks and colours.
+- Changes from Bravado to requests to improve download performance.
+- Changes `ping` command to perform user access token validation.
+- Changes defaults to accept both `reana.yaml` and `reana.yml` filenames.
+- Changes `diff` command to improve output formatting.
+- Changes code formatting to respect `black` coding style.
+- Changes documentation to single-page layout.
+
+## 0.6.1 (2020-06-09)
+
+- Fixes installation troubles for REANA 0.6.x release series by pinning several
+  dependencies.
+
+## 0.6.0 (2019-12-27)
+
+- Introduces user secrets management commands `secrets-add`,
+  `secrets-list` and `secrets-delete`.
+- Enhances `run` and `create` commands to allow specifying
+  workfow via the `--workflow` flag.
+- Introduces new command `version` to report client version.
+- Fixes `upload` command behaviour for uploading very large files.
+- Simplifies `run` command by removing free upload parameters.
+- Upgrades `cwltool` to 1.0.20191022103248.
+- Disables SSL verification warnings when talking to self-signed server
+  certificates.
+
+## 0.5.0 (2019-04-24)
+
+- Introduces new `resources` field in `reana.yaml` specification file
+  allowing to declare computing resources needed for workflow runs, such as the
+  CVMFS repositories via `cvmfs` subfield.
+- Improves `reana-client` embedded command-line documentation (`-help`) by
+  grouping commands and providing concrete usage examples for all commands.
+- Enhances workflow `start` command allowing to override input parameters
+  (`--parameter`) and to specify additional operational options
+  (`--option`).
+- Introduces new workflow `run` wrapper command that creates workflow, uploads
+  its input data and code and starts its execution.
+- Introduces new workflow `stop` command for stopping a running workflow.
+- Enhances workflow `logs` command output capabilities via new `--json`
+  option.
+- Introduces new workflow `diff` command for comparing two workflow runs.
+- Introduces new workflow `delete` command for deleting one or more workflow
+  runs.
+- Introduces new session `open` command allowing to run interactive sessions
+  such as Jupyter notebook upon workflow workspace.
+- Introduces new session `close` command for closing interactive sessions.
+- Renames past `workflows` command to `list` allowing to list both workflow
+  runs and interactive sessions.
+- Introduces new workspace `du` command for checking workspace disk usage.
+- Introduces new workspace `mv` command for moving files within workspace.
+- Introduces new workspace `rm` command for removing files within workspace.
+- Renames past workspace `list` command to `ls` allowing to list workspace
+  files. Enhances its output capabilities via new `--format` option.
+- Introduces new API function `create_workflow_from_json()` which allows
+  developers and third-party systems to create workflows directly from JSON
+  specification.
+
+## 0.4.0 (2018-11-07)
+
+- Enhances test suite and increases code coverage.
+- Changes license to MIT.
+
+## 0.3.1 (2018-09-25)
+
+- Amends upload and download commands that will now upload/download all the
+  files specified in `reana.yaml` in case no arguments are provided.
+- Fixes `status` command's JSON output mode.
+- Upgrades CWL reference implementation to version `1.0.20180912090223`.
+- Renames Serial workflow operational parameter from ``` CACHING``to ``CACHE ```.
+- Adds support for Python 3.7.
+
+## 0.3.0 (2018-08-10)
+
+- Adds support for
+  [Serial workflows](http://reana-workflow-engine-serial.readthedocs.io/en/latest/).
+
+- CLI refactored to a flat design:
+
+  - `inputs`/`outputs`/`code` removed, everything is a file managed
+    : with upload/download/list commands.
+  - Removes `workflow` command, workflows are managed with
+    : `create`/`start`/`status`.
+
+- Removes `analyes` command, now `validate` is first level command.
+
+- `status` now shows the selected workflow progress and current command on
+  verbose mode.
+
+- Requires the usage of an access token to talk to REANA Server.
+
+- Fixes bug when uploading binary files.
+
+- Supports addition of workflow engine parameters when using `start` for
+  serial workflows.
+
+- Improves error messages.
+
+## 0.2.0 (2018-04-20)
+
+- Adds support for Common Workflow Language workflows.
+- Adds support for persistent user-selected workflow names.
+- Enables file and directory input uploading using absolute paths.
+- Adds new `status` command to display the current status of the client.
+- Reduces verbosity level for commands and improves error messages.
+
+## 0.1.0 (2018-01-30)
+
+- Initial public release.
+